The steamer captured the blockade runner Thistle in June and took the runner Boston as prize during the next month. The success of her voyage was heightened when in the same period she plucked drifting cotton bales and bags from the sea and sent them to Philadelphia for adjudication.

During October she was attached to the 2nd Division North Atlantic Blockading Squadron and on 21 October captured CSS Wando attempting to run through with a cargo of cotton.

During December Fort Jackson fought in the battle off Wilmington and in the first bombardment of Fort Fisher (24–25 December) during which she covered troop landings and received on board the dead and wounded.